The article provides information about the sanitary-bacteriological studies conducted in the water area of Lake Baikal. We show the data on the long-term observations of the spread and abundance of fecal indicator bacteria and potentially pathogenic bacteria in the pelagic and littoral waters of the lake. We also present a review of the standards and methods for the sanitary-bacteriological water quality worldwide, techniques for detecting fecal indicator bacteria, including those specific for human microbiota, methods for microbial source tracking, as well as studies of the spread and retaining of fecal indicator bacteria in various ecotopes, such as bottom sediments and biofilms. For the sanitarybacteriological monitoring of Lake Baikal, we propose an integrated approach based on the application of modern techniques that correspond to world practice. This approach would allow identification of the sanitary adverse sites and more reliable and standardized assessment of the Baikal water quality.